def post_serializer(obj, level_name="", general_handler=None):
if isinstance(obj, dict) and not hasattr(obj, 'serializer'):
from webfront.views.entry import filter_entry_overview
from webfront.views.structure import filter_structure_overview
if "entries" in obj:
obj["entries"] = filter_entry_overview(obj["entries"], general_handler, "protein")
if "structures" in obj:
obj["structures"] = filter_structure_overview(obj["structures"], general_handler, "protein")
else:
if not isinstance(obj.serializer, ProteinSerializer):
prots = [x[0]
for x in general_handler.queryset_manager.get_queryset("protein")
.values_list("accession").distinct()]
remove_empty_structures = False
arr = [obj] if isinstance(obj, dict) else obj
for o in arr:
if "proteins" in o:
o["proteins"] = [p for p in o["proteins"]
if level_name in prots and(
(("accession" in p and p["accession"] == level_name) or
("protein" in p and p["protein"]["accession"] == level_name)))]
if len(o["proteins"]) == 0:
remove_empty_structures = True
if remove_empty_structures:
arr = [a for a in arr if len(a["proteins"]) > 0]
if len(arr) == 0:
raise ReferenceError("The entry {} doesn't exist in the selected url".format(level_name))
return obj
def post_serializer(obj, level_name="", general_handler=None):
if isinstance(obj, dict) and not hasattr(obj, "serializer"):
from webfront.views.entry import filter_entry_overview
from webfront.views.protein import filter_protein_overview
if "entries" in obj:
obj["entries"] = filter_entry_overview(obj["entries"], general_handler, "structure")
if "proteins" in obj:
obj["proteins"] = filter_protein_overview(obj["proteins"], general_handler, "structure")
else:
if not isinstance(obj.serializer, StructureSerializer):
arr = obj
if isinstance(obj, dict):
arr = [obj]
for o in arr:
if "structures" in o:
o["structures"] = [
p
for p in o["structures"]
if ("accession" in p and p["accession"] == level_name)
or (
"structure" in p
and "accession" in p["structure"]
and p["structure"]["accession"] == level_name
)
]
return obj
def post_serializer(obj, level_name="", general_handler=None):
if isinstance(obj, dict) and not hasattr(obj, 'serializer'):
from webfront.views.entry import filter_entry_overview
from webfront.views.structure import filter_structure_overview
if "entries" in obj:
obj["entries"] = filter_entry_overview(obj["entries"], general_handler, "protein")
if "structures" in obj:
obj["structures"] = filter_structure_overview(obj["structures"], general_handler, "protein")
return obj
prots = [x[0]
for x in general_handler.queryset_manager.get_queryset("protein")
.values_list("accession").distinct()]
if hasattr(obj, 'serializer') and not isinstance(obj.serializer, ProteinSerializer):
remove_empty_structures = False
arr = obj if isinstance(obj, list) else [obj]
for o in arr:
if "proteins" in o:
o["proteins"] = [p
for p in o["proteins"]
if (level_name == "uniprot" or
("source_database"in p and p["source_database"] == level_name)) and
(prots is None or p["accession"] in prots)]
if len(o["proteins"]) == 0:
remove_empty_structures = True
if remove_empty_structures:
arr = [a for a in arr if len(a["proteins"]) > 0]
if len(arr) == 0:
raise ReferenceError("There are not proteins fo the database {} with the selected filters"
.format(level_name))
return obj
def post_serializer(obj, level_name="", general_handler=None):
if isinstance(obj, dict) and not hasattr(obj, "serializer"):
from webfront.views.entry import filter_entry_overview
from webfront.views.protein import filter_protein_overview
if "entries" in obj:
obj["entries"] = filter_entry_overview(obj["entries"], general_handler, "structure")
if "proteins" in obj:
obj["proteins"] = filter_protein_overview(obj["proteins"], general_handler, "structure")
return obj
try:
structures = [
x[0]
for x in general_handler.queryset_manager.get_queryset("structure").values_list("accession").distinct()
]
arr = [obj] if isinstance(obj, dict) else obj
for result in arr:
result["structures"] = [x for x in result["structures"] if x["accession"] in structures]
finally:
return obj
def post_serializer(obj, level_name="", general_handler=None):
if isinstance(obj, dict) and not hasattr(obj, "serializer"):
from webfront.views.entry import filter_entry_overview
from webfront.views.protein import filter_protein_overview
if "entries" in obj:
obj["entries"] = filter_entry_overview(obj["entries"], general_handler, "structure")
if "proteins" in obj:
obj["proteins"] = filter_protein_overview(obj["proteins"], general_handler, "structure")
else:
pdb = general_handler.get_from_store(PDBAccessionHandler, "pdb_accession")
arr = obj
remove_empty_structures = False
if isinstance(obj, dict):
arr = [obj]
for o in arr:
if "structures" in o:
o["structures"] = [
p
for p in o["structures"]
if ("chain" in p and p["chain"] == level_name and p["structure"]["accession"] == pdb)
or (
"structure" in p
and "chain" in p["structure"]
and p["structure"]["chain"] == level_name
and p["structure"]["accession"] == pdb
)
]
if len(o["structures"]) == 0:
remove_empty_structures = True
if (
"entries" in o
and isinstance(o["entries"], list)
and len(o["entries"]) > 0
and "chain" in o["entries"][0]
):
o["entries"] = [
p
for p in o["entries"]
if ("chain" in p and p["chain"] == level_name)
or ("structure" in p and "chain" in p["structure"] and p["entry"]["chain"] == level_name)
]
if len(o["entries"]) == 0:
raise ReferenceError("The chain {} doesn't exist in the selected structure".format(level_name))
if (
"proteins" in o
and isinstance(o["proteins"], list)
and len(o["proteins"]) > 0
and "chain" in o["proteins"][0]
):
o["proteins"] = [
p
for p in o["proteins"]
if ("chain" in p and p["chain"] == level_name)
or ("structure" in p and "chain" in p["structure"] and p["entry"]["chain"] == level_name)
]
if len(o["proteins"]) == 0:
raise ReferenceError("The chain {} doesn't exist in the selected structure".format(level_name))
if "metadata" in o and "chains" in o["metadata"] and isinstance(o["metadata"]["chains"], dict):
o["metadata"]["chains"] = {
p: o["metadata"]["chains"][p] for p in o["metadata"]["chains"] if (level_name in p)
}
if remove_empty_structures:
arr = [a for a in arr if len(a["structures"]) > 0]
if len(arr) == 0:
raise ReferenceError("The chain {} doesn't exist in the selected structure".format(level_name))
return arr
return obj
